Inflammation can be beneficial for a normal immune response to microbial pathogens. However, prolonged inflammation can promote tissue damage during infection and has been closely linked to a diverse range of diseases, including cancer, atherosclerosis, and several inflammatory autoimmune diseases. Although a number of anti-inflammatory drugs are available, none of them are considered to be ideal for a variety of reasons, including insufficient target specificity and limited potency. Therefore, new strategies are needed for the development of inhibitors of pro-inflammatory genes and proteins. One major limitation in pursuing pharmaceuticals that inhibit the transcription of specific pro-inflammatory genes is that our understanding of the molecular mechanisms responsible for selective gene regulation remains rudimentary. Transcription factors such as NF-?B and AP-1 contribute to the activation of many pro-inflammatory genes. However, because of their broad functions, these factors may not be appropriate targets for the inhibition of specific subsets of inducible genes. During the past few years, a number of signal transduction pathways activated by Toll-like receptors (TLRs) and other transmembrane receptors have been elucidated, resulting in great strides toward the identification of pathways that lead to selective gene regulation. However, it will be difficult to fully appreciate the mechanisms responsible for the differential regulation of pro-inflammatory genes without an understanding of the logical organization of the control regions and DNA sequence elements associated with these genes. Our laboratory has found that genes induced by lipopolysaccharide (LPS) in murine macrophages can be divided into six broad classes on the basis of several criteria, including their (1) requirement for new protein synthesis, (2) requirement for nucleosome remodeling by the SWI/SNF family of ATP-dependent nucleosome remodeling complexes, (3) requirement for the transcription factor IRF3, and (4) the presence of a CpG island promoter. The experiments proposed in this application focus on the four classes of primary response genes, which are defined as genes directly activated by LPS signaling pathways in the absence of new protein synthesis. The proposed experiments will examine a variety of hypotheses, including the hypothesis that the critical properties of primary response genes are stimulus-specific and the hypothesis that CpG islands are frequently associated with SWI/SNF-independent primary response genes because the high CpG-content is incompatible with the assembly of stable nucleosomes. We will also examine the role of IRF3 in the activation of a specific class of SWI/SNF-dependent primary response genes. Finally, we will make use of bacterial artificial chromosomes containing representative members of each gene class to initiate more detailed analyses of the diverse activation mechanisms. Together, these studies should greatly expand our knowledge of the selective regulation of pro-inflammatory genes in cells of the innate immune system. PUBLIC HEALTH RELEVANCE: The aberrant expression of specific pro-inflammatory genes plays a major role in a number of common diseases, including cancer, atherosclerosis, and a number of inflammatory autoimmune disorders. Significantly, recent studies have shown that enhanced expression of some inflammatory genes helps protect against disease, whereas other genes enhance disease progression. The objective of the proposed research is to better understand the molecular mechanisms regulating the differential expression of inflammatory genes in cells of the immune system. The long-term goal of this research is to develop pharmacologic strategies for the selective modulation of pro-inflammatory genes, leading to the enhanced expression of protective genes and reduced expression of detrimental genes.